[gmx-users] Editconf error

Jorge Dagnino jdagnino at gmail.com
Fri May 22 22:07:59 CEST 2015


Here are the complete files.

pdb2gmx input: http://pastebin.com/HBmrR0eF

.gro output: http://paste2.org/ahY6MB99

editconf input: http://paste2.org/9fPp6J02

editconf output: http://paste2.org/v1IsPp6O

Thanks.

2015-05-22 16:21 GMT-03:00 Barnett, James W <jbarnet4 at tulane.edu>:

> It'd be more helpful for troubleshooting your problem if you post the
> entire file in each case, not just parts of them. If it's a large file use
> Pastebin.com or something similar.
>
> --
> James "Wes" Barnett
> Ph.D. Candidate
> Chemical and Biomolecular Engineering
>
> Tulane University
> Boggs Center for Energy and Biotechnology, Room 341-B
> New Orleans, Louisiana 70118
> jbarnet4 at tulane.edu> LinkedIn​​
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Jorge
> Dagnino <jdagnino at gmail.com>
> Sent: Friday, May 22, 2015 11:06 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Editconf error
>
> Here are the coordinates from my pdb file:
>
> ATOM      1  N   MET G  27      69.331  43.147  76.443  1.00  0.00
>   N
> ATOM      2  CA  MET G  27      68.996  44.047  75.331  1.00  0.00
>   C
> ATOM      3  C   MET G  27      67.818  43.550  74.510  1.00  0.00
>   C
> ATOM      4  O   MET G  27      66.981  44.264  73.969  1.00  0.00
>   O
> ATOM      5  CB  MET G  27      70.152  44.201  74.325  1.00  0.00
>   C
> ATOM      6  CG  MET G  27      70.024  45.547  73.614  1.00  0.00
>   C
> ATOM      7  SD  MET G  27      70.710  46.841  74.678  1.00  0.00
>   S
> ATOM      8  CE  MET G  27      70.252  48.118  73.481  1.00  0.00
>   C
> ATOM      9  N   ALA G  28      67.504  42.250  74.523  1.00  0.00
>   N
> ATOM     10  CA  ALA G  28      66.247  41.666  74.095  1.00  0.00
>   C
> ATOM     11  C   ALA G  28      64.968  42.391  74.469  1.00  0.00
>   C
> ATOM     12  O   ALA G  28      64.064  42.543  73.651  1.00  0.00
>   O
> ATOM     13  CB  ALA G  28      66.323  40.167  74.396  1.00  0.00
>   C
> ATOM     14  N   GLU G  29      64.839  42.732  75.756  1.00  0.00
>   N
> ATOM     15  CA  GLU G  29      63.656  43.315  76.334  1.00  0.00
>   C
> ATOM     16  C   GLU G  29      63.567  44.789  75.955  1.00  0.00
>   C
> ATOM     17  O   GLU G  29      62.480  45.354  75.850  1.00  0.00
>   O
> ATOM     18  CB  GLU G  29      63.662  43.143  77.854  1.00  0.00
>   C
> ATOM     19  CG  GLU G  29      64.822  43.835  78.553  1.00  0.00
>   C
> ATOM     20  CD  GLU G  29      64.794  43.644  80.055  1.00  0.00
>   C
> ATOM     21  OE1 GLU G  29      63.801  44.058  80.689  1.00  0.00
>   O
> ATOM     22  OE2 GLU G  29      65.765  43.078  80.601  1.00  0.00
>   O1-
>
> And here are the coordinates from the .gro file
>
> Giant Rising Ordinary Mutants for A Clerical Setup
> 16231
>    27MET      N    1   6.933   4.315   7.644
>    27MET     H1    2   7.011   4.352   7.695
>    27MET     H2    3   6.854   4.307   7.705
>    27MET     H3    4   6.957   4.224   7.608
>    27MET     CA    5   6.900   4.405   7.533
>    27MET     HA    6   6.878   4.489   7.582
>    27MET     CB    7   7.015   4.420   7.432
>    27MET    HB1    8   7.103   4.416   7.481
>    27MET    HB2    9   7.011   4.346   7.365
>    27MET     CG   10   7.002   4.555   7.361
>    27MET    HG1   11   7.052   4.545   7.275
>    27MET    HG2   12   6.905   4.567   7.343
>    27MET     SD   13   7.071   4.684   7.468
>    27MET     CE   14   7.025   4.812   7.348
>    27MET    HE1   15   7.053   4.901   7.383
>    27MET    HE2   16   7.071   4.794   7.261
>    27MET    HE3   17   6.926   4.811   7.334
>    27MET      C   18   6.782   4.355   7.451
>    27MET      O   19   6.698   4.426   7.397
>    28ALA      N   20   6.750   4.225   7.452
>    28ALA      H   21   6.820   4.162   7.486
>    28ALA     CA   22   6.625   4.167   7.410
>    28ALA     HA   23   6.620   4.184   7.311
>    28ALA     CB   24   6.632   4.017   7.440
>    28ALA    HB1   25   6.547   3.973   7.411
>    28ALA    HB2   26   6.709   3.976   7.389
>    28ALA    HB3   27   6.646   4.003   7.538
>    28ALA      C   28   6.497   4.239   7.447
>    28ALA      O   29   6.406   4.254   7.365
>    29GLU      N   30   6.484   4.273   7.576
>    29GLU      H   31   6.562   4.257   7.636
>    29GLU     CA   32   6.366   4.332   7.633
>    29GLU     HA   33   6.289   4.281   7.594
>    29GLU     CB   34   6.366   4.314   7.785
>    29GLU    HB1   35   6.281   4.352   7.822
>    29GLU    HB2   36   6.371   4.217   7.806
>    29GLU     CG   37   6.482   4.384   7.855
>    29GLU    HG1   38   6.568   4.346   7.820
>    29GLU    HG2   39   6.478   4.481   7.836
>    29GLU     CD   40   6.479   4.364   8.005
>    29GLU    OE1   41   6.380   4.406   8.069
>    29GLU    OE2   42   6.576   4.308   8.060
>    29GLU      C   43   6.357   4.479   7.595
>    29GLU      O   44   6.248   4.535   7.585
>
> and this is the output from editconf.
>
> Giant Rising Ordinary Mutants for A Clerical Setup
> 16231
>    27MET      N    1    -nan    -nan    -nan
>    27MET     H1    2    -nan    -nan    -nan
>    27MET     H2    3    -nan    -nan    -nan
>    27MET     H3    4    -nan    -nan    -nan
>    27MET     CA    5    -nan    -nan    -nan
>    27MET     HA    6    -nan    -nan    -nan
>    27MET     CB    7    -nan    -nan    -nan
>    27MET    HB1    8    -nan    -nan    -nan
>    27MET    HB2    9    -nan    -nan    -nan
>    27MET     CG   10    -nan    -nan    -nan
>    27MET    HG1   11    -nan    -nan    -nan
>    27MET    HG2   12    -nan    -nan    -nan
>    27MET     SD   13    -nan    -nan    -nan
>    27MET     CE   14    -nan    -nan    -nan
>    27MET    HE1   15    -nan    -nan    -nan
>    27MET    HE2   16    -nan    -nan    -nan
>    27MET    HE3   17    -nan    -nan    -nan
>    27MET      C   18    -nan    -nan    -nan
>    27MET      O   19    -nan    -nan    -nan
>
> I hope that this helps.
> Thanks
>
>
> 2015-05-20 22:28 GMT-03:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 5/20/15 5:27 PM, Jorge Dagnino wrote:
> >
> >> Dear GMX users.
> >>
> >> Im trying to create my system and When i use pdb2gmx everything seems
> ok.
> >>
> >> gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id
> >>
> >> Including chain 1 in system: 3235 atoms 203 residues
> >> Including chain 2 in system: 2531 atoms 161 residues
> >> Including chain 3 in system: 2546 atoms 161 residues
> >> Including chain 4 in system: 2531 atoms 161 residues
> >> Including chain 5 in system: 2546 atoms 161 residues
> >> Including chain 6 in system: 2842 atoms 169 residues
> >> Now there are 16231 atoms and 1016 residues
> >> Total mass in system 115288.734 a.m.u.
> >> Total charge in system -17.000 e
> >>
> >> Writing coordinate file...
> >>
> >> --------- PLEASE NOTE ------------
> >> You have successfully generated a topology from: trim.pdb.
> >> The OplsaaPBS force field and the spce water model are used.
> >>
> >> Then when i use the editconf command :
> >>
> >> gmx editconf -f trim.gro -bt dodecahedron -o box -c -d 1.0
> >>
> >>
> >> Read 16231 atoms
> >> Volume: 60.3503 nm^3, corresponds to roughly 27100 electrons
> >> No velocities found
> >>      system size : 11.777 11.005  6.369 (nm)
> >>      diameter    : 12.737               (nm)
> >>      center      :   -nan   -nan   -nan (nm)
> >>      box vectors :  4.144  4.582  3.178 (nm)
> >>      box angles  :  90.00  90.00  90.00 (degrees)
> >>      box volume  :  60.35               (nm^3)
> >>      shift       :   -nan   -nan   -nan (nm)
> >> new center      :   -nan   -nan   -nan (nm)
> >> new box vectors : 14.737 14.737 14.737 (nm)
> >> new box angles  :  60.00  60.00  90.00 (degrees)
> >> new box volume  :2262.99               (nm^3)
> >>
> >> and the ouptut file looks like this.
> >>
> >> Giant Rising Ordinary Mutants for A Clerical Setup
> >> 16231
> >>     27MET      N    1    -nan    -nan    -nan
> >>     27MET     H1    2    -nan    -nan    -nan
> >>     27MET     H2    3    -nan    -nan    -nan
> >>     27MET     H3    4    -nan    -nan    -nan
> >>     27MET     CA    5    -nan    -nan    -nan
> >>
> >> I try to make a bigger box manually, also change the box shape and the
> >> distance but i have the same result,
> >> This is my first time with this kind of error, what is wrong? what am i
> >> missing?
> >>
> >
> > Hard to say; I've never seen anything like this.  The 'nan' means "not a
> > number" so the coordinates are junk.  Are the coordinates in trim.pdb and
> > trim.gro sound?
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
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> >
>
>
>
> --
> JORGE DAGNINO LEONE
> Bioquímico
> Magíster en Bioquímica y Bioinformática
> Estudiante de Doctorado en Ciencias Biológicas.
> Facultad de Ciencias Biológicas
> Laboratorio de Biofísica Molecular
> Universidad de Concepción
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-- 
JORGE DAGNINO LEONE
Bioquímico
Magíster en Bioquímica y Bioinformática
Estudiante de Doctorado en Ciencias Biológicas.
Facultad de Ciencias Biológicas
Laboratorio de Biofísica Molecular
Universidad de Concepción


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